RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

Eric Lewitus; Eric Sanders-Buell; Meera Bose; Anne Marie O’Sullivan; Kultida Poltavee; Yifan Li; Hongjun Bai; Thembi Mdluli; Gina Donofrio; Bonnie Slike; Hong Zhao; Kim Wong; Lennie Chen; Shana Miller; Jenica Lee; Bahar Ahani; Steven Lepore; Sevan Muhammad; Rebecca Grande; Ursula Tran; Vincent Dussupt; Letzibeth Mendez-Rivera; Sorachai Nitayaphan; Jaranit Kaewkungwal; Punnee Pitisuttithum; Supachai Rerks-Ngarm; Robert J. O’Connell; Holly Janes; Peter B. Gilbert; Robert Gramzinski; Sandhya Vasan; Merlin L. Robb; Nelson L. Michael; Shelly J. Krebs; Joshua T. Herbeck; Paul T. Edlefsen; James I. Mullins; Jerome H. Kim; Sodsai Tovanabutra; Morgane Rolland

doi:10.1093/ve/veab057

RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

Eric Lewitus, Eric Sanders-Buell, Meera Bose, Anne Marie O’Sullivan, Kultida Poltavee, Yifan Li, Hongjun Bai, Thembi Mdluli, Gina Donofrio, Bonnie Slike, Hong Zhao, Kim Wong, Lennie Chen, Shana Miller, Jenica Lee, Bahar Ahani, Steven Lepore, Sevan Muhammad, Rebecca Grande, Ursula TranVincent Dussupt, Letzibeth Mendez-Rivera, Sorachai Nitayaphan, Jaranit Kaewkungwal, Punnee Pitisuttithum, Supachai Rerks-Ngarm, Robert J. O’Connell, Holly Janes, Peter B. Gilbert, Robert Gramzinski, Sandhya Vasan, Merlin L. Robb, Nelson L. Michael, Shelly J. Krebs, Joshua T. Herbeck, Paul T. Edlefsen, James I. Mullins, Jerome H. Kim, Sodsai Tovanabutra, Morgane Rolland^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1’s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.

Original language	English
Article number	A1349
Journal	Virus Evolution
Volume	7
Issue number	2
DOIs	https://doi.org/10.1093/ve/veab057
State	Published - 2021
Externally published	Yes

Keywords

HIV-1
Sieve analysis
Vaccine
Within-host evolution

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10.1093/ve/veab057

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Lewitus, E., Sanders-Buell, E., Bose, M., O’Sullivan, A. M., Poltavee, K., Li, Y., Bai, H., Mdluli, T., Donofrio, G., Slike, B., Zhao, H., Wong, K., Chen, L., Miller, S., Lee, J., Ahani, B., Lepore, S., Muhammad, S., Grande, R., ... Rolland, M. (2021). RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection. Virus Evolution, 7(2), Article A1349. https://doi.org/10.1093/ve/veab057

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title = "RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection",

abstract = "The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1{\textquoteright}s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.",

keywords = "HIV-1, Sieve analysis, Vaccine, Within-host evolution",

author = "Eric Lewitus and Eric Sanders-Buell and Meera Bose and O{\textquoteright}Sullivan, {Anne Marie} and Kultida Poltavee and Yifan Li and Hongjun Bai and Thembi Mdluli and Gina Donofrio and Bonnie Slike and Hong Zhao and Kim Wong and Lennie Chen and Shana Miller and Jenica Lee and Bahar Ahani and Steven Lepore and Sevan Muhammad and Rebecca Grande and Ursula Tran and Vincent Dussupt and Letzibeth Mendez-Rivera and Sorachai Nitayaphan and Jaranit Kaewkungwal and Punnee Pitisuttithum and Supachai Rerks-Ngarm and O{\textquoteright}Connell, {Robert J.} and Holly Janes and Gilbert, {Peter B.} and Robert Gramzinski and Sandhya Vasan and Robb, {Merlin L.} and Michael, {Nelson L.} and Krebs, {Shelly J.} and Herbeck, {Joshua T.} and Edlefsen, {Paul T.} and Mullins, {James I.} and Kim, {Jerome H.} and Sodsai Tovanabutra and Morgane Rolland",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2021. Published by Oxford University Press.",

year = "2021",

doi = "10.1093/ve/veab057",

language = "English",

volume = "7",

journal = "Virus Evolution",

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Lewitus, E, Sanders-Buell, E, Bose, M, O’Sullivan, AM, Poltavee, K, Li, Y, Bai, H, Mdluli, T, Donofrio, G, Slike, B, Zhao, H, Wong, K, Chen, L, Miller, S, Lee, J, Ahani, B, Lepore, S, Muhammad, S, Grande, R, Tran, U, Dussupt, V, Mendez-Rivera, L, Nitayaphan, S, Kaewkungwal, J, Pitisuttithum, P, Rerks-Ngarm, S, O’Connell, RJ, Janes, H, Gilbert, PB, Gramzinski, R, Vasan, S, Robb, ML, Michael, NL, Krebs, SJ, Herbeck, JT, Edlefsen, PT, Mullins, JI, Kim, JH, Tovanabutra, S & Rolland, M 2021, 'RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection', Virus Evolution, vol. 7, no. 2, A1349. https://doi.org/10.1093/ve/veab057

TY - JOUR

T1 - RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

AU - Lewitus, Eric

AU - Sanders-Buell, Eric

AU - Bose, Meera

AU - O’Sullivan, Anne Marie

AU - Poltavee, Kultida

AU - Li, Yifan

AU - Bai, Hongjun

AU - Mdluli, Thembi

AU - Donofrio, Gina

AU - Slike, Bonnie

AU - Zhao, Hong

AU - Wong, Kim

AU - Chen, Lennie

AU - Miller, Shana

AU - Lee, Jenica

AU - Ahani, Bahar

AU - Lepore, Steven

AU - Muhammad, Sevan

AU - Grande, Rebecca

AU - Tran, Ursula

AU - Dussupt, Vincent

AU - Mendez-Rivera, Letzibeth

AU - Nitayaphan, Sorachai

AU - Kaewkungwal, Jaranit

AU - Pitisuttithum, Punnee

AU - Rerks-Ngarm, Supachai

AU - O’Connell, Robert J.

AU - Janes, Holly

AU - Gilbert, Peter B.

AU - Gramzinski, Robert

AU - Vasan, Sandhya

AU - Robb, Merlin L.

AU - Michael, Nelson L.

AU - Krebs, Shelly J.

AU - Herbeck, Joshua T.

AU - Edlefsen, Paul T.

AU - Mullins, James I.

AU - Kim, Jerome H.

AU - Tovanabutra, Sodsai

AU - Rolland, Morgane

PY - 2021

Y1 - 2021

N2 - The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1’s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.

AB - The scale of the HIV-1 epidemic underscores the need for a vaccine. The multitude of circulating HIV-1 strains together with HIV-1’s high evolvability hints that HIV-1 could adapt to a future vaccine. Here, we wanted to investigate the effect of vaccination on the evolution of the virus post-breakthrough infection. We analyzed 2,635 HIV-1 env sequences sampled up to a year post-diagnosis from 110 vaccine and placebo participants who became infected in the RV144 vaccine efficacy trial. We showed that the Env signature sites that were previously identified to distinguish vaccine and placebo participants were maintained over time. In addition, fewer sites were under diversifying selection in the vaccine group than in the placebo group. These results indicate that HIV-1 would possibly adapt to a vaccine upon its roll-out.

KW - HIV-1

KW - Sieve analysis

KW - Vaccine

KW - Within-host evolution

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U2 - 10.1093/ve/veab057

DO - 10.1093/ve/veab057

M3 - Article

AN - SCOPUS:85116532627

SN - 2057-1577

VL - 7

JO - Virus Evolution

JF - Virus Evolution

IS - 2

M1 - A1349

ER -

RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection

Abstract

Keywords

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